tsSample-class {TargetSearch} | R Documentation |
This is a class to represent a set of samples.
Objects can be created by the function ImportSamples
or by calling
the object generator function.
new("tsSample", Names = [sample names], CDFfiles = [list of CDF file names],
RIfiles = [list of RI file names], CDFpath = [CDF files path],
RIpath = [RI files path], days = [measurement days],
data = [additional sample information], ftype = [RI file format])
Names
:"character"
, the sample names.
CDFfiles
:"character"
, the list of CDF file names.
RIfiles
:"character"
, the list of RI file names.
CDFpath
:"character"
, CDF files path.
RIpath
:"character"
, RI file path.
days
:"character"
, measurement days.
data
:"data.frame"
, additional sample information.
[
signature(x = "tsSample")
: Selects a subset of samples.
$name
signature(x = "tsSample")
: Access column name
of sampleData
slot.
CDFfiles
signature(obj = "tsSample")
: list of CDF files.
RIfiles
signature(obj = "tsSample")
: list of RI files.
RIpath
signature(obj = "tsSample")
: The RI file path.
CDFpath
signature(obj = "tsSample")
: The CDF file path.
length
signature(x = "tsSample")
: number of samples.
sampleData
signature(obj = "tsSample")
: additional sample information.
sampleDays
signature(obj = "tsSample")
: measurement days.
sampleNames
signature(obj = "tsSample")
: sample names. The names must be unique
show
signature(object = "tsSample")
: the show funtion.
fileFormat
signature
obj = "tsSample": Sets or gets the RI file format.
Options are either "binary" or "text". See note below.
The method fileFormat
only changes the internal information
of the file type and not the files themselves. To actually
change the files, use the functions bin2text
and text2bin
.
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
showClass("tsSample") # get a list of CDF files from a directory require(TargetSearchData) CDFpath <- system.file("gc-ms-data", package = "TargetSearchData") cdffiles <- dir(CDFpath, "cdf") # define the RI file path RIpath <- "." # create the sample object sampleDescription <- new("tsSample", CDFfiles = cdffiles, CDFpath = CDFpath, RIpath = RIpath) ## # More parameters could be defined: # define the RI files and the RI path RIfiles <- sub("cdf$", "txt", paste("RI_", cdffiles, sep = "")) RIpath <- "." # get the measurement days (the four first numbers of the cdf files, in this # example) days <- substring(cdffiles, 1, 4) # sample names smp_names <- sub(".cdf", "", cdffiles, fixed = TRUE) # add some sample info smp_data <- data.frame(CDF_FILE =cdffiles, GROUP = gl(5,3)) # create the sample object sampleDescription <- new("tsSample", Names = smp_names, CDFfiles = cdffiles, CDFpath = CDFpath, RIpath = RIpath, days = days, RIfiles = RIfiles, data = smp_data) # changing the sample names sampleNames(sampleDescription) <- paste("Sample", 1:length(sampleDescription), sep = "_") # changing the file paths (relative to the working path) CDFpath(sampleDescription) <- "my_cdfs/" RIpath(sampleDescription) <- "my_RIs/"